title: Computational modeling of protein-RNA complex structures.
abstract: Protein-RNA interactions play fundamental roles in many biological processes, such as regulation of gene expression, RNA splicing, and protein synthesis. The understanding of these processes improves as new structures of protein-RNA complexes are solved and the molecular details of interactions analyzed. However, experimental determination of protein-RNA complex structures by high-resolution methods is tedious and difficult. Therefore, studies on protein-RNA recognition and complex formation present major technical challenges for macromolecular structural biology. Alternatively, protein-RNA interactions can be predicted by computational methods. Although less accurate than experimental measurements, theoretical models of macromolecular structures can be sufficiently accurate to prompt functional hypotheses and guide e.g. identification of important amino acid or nucleotide residues. In this article we present an overview of strategies and methods for computational modeling of protein-RNA complexes, including software developed in our laboratory, and illustrate it with practical examples of structural predictions.
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: irena@genesilico.pl.
authors.forename: Irina
authors.initials: I
authors.lastname: Tuszynska
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: dmatelska@genesilico.pl.
authors.forename: Dorota
authors.initials: D
authors.lastname: Matelska
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: magnus@genesilico.pl.
authors.forename: Marcin
authors.initials: M
authors.lastname: Magnus
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: gchojnowski@genesilico.pl.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Chojnowski
authors.affiliation: Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland. Electronic address: jkasp@amu.edu.pl.
authors.forename: Joanna M
authors.initials: JM
authors.lastname: Kasprzak
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: lukaskoz@genesilico.pl.
authors.forename: Lukasz P
authors.initials: LP
authors.lastname: Kozlowski
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: sdh@genesilico.pl.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland; Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland. Electronic address: iamb@genesilico.pl.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
mesh_terms: D001412:Bacillus subtilis / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D011485:Protein Binding; D012336:RNA, Ribosomal, 16S / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D058928:Riboswitch / Q000235:genetics*; D012984:Software; D046968:Thermoanaerobacter / Q000737:chemistry
chemical_list: D029968:Escherichia coli Proteins; D012336:RNA, Ribosomal, 16S; D016601:RNA-Binding Proteins; D058928:Riboswitch
keywords: Computational docking; Macromolecular complex; Protein; Protein–RNA binding; RNA; RNP; Structural bioinformatics